Runt-related (RUNX) transcription factors are evolutionarily conserved regulators of cell proliferation, differentiation and stem cell maintenance. They are critical for the correct development and function of a variety of human tissues, including during haematopoiesis. RUNX genes regulate various aspects of proliferation control, stem cell maintenance, lineage commitment and regulation of differentiation; disruptions in the correct function of RUNX genes have been associated with human pathologies, most prominently cancer. Because of the high context dependency and partial redundancy of vertebrate RUNX genes, invertebrate model systems have been studied in the hope of finding an ancestral function. Here we review the progress of these studies in three invertebrate systems, the fruit fly Drosophila melanogaster, the sea urchin Strongylocentrotus purpuratus and the nematode Caenorhabditis elegans. All essential aspects of RUNX function in vertebrates have counterparts in invertebrates, confirming the usefulness of these studies in simpler organisms. The fact that not all RUNX functions are conserved in all systems, though, underscores the importance of choosing the right model to ask specific questions.